3KX3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BACILLUS MEGATERIUM BM3 HEME DOMAIN MUTANT L86E

Authors :   H. M. Girvan, C. W. Levy, D. Leys, A. W. Munro

Date :   02 Dec 09 (Deposition) - 19 May 10 (Release) - 19 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Cytochrome P450, L86E Mutant, Heme Domain, Cytoplasm, Electron Transport, Fad, Flavoprotein, Fmn, Heme, Iron, Metal-Binding, Monooxygenase, Multifunctional Enzyme, Nadp, Oxidoreductase, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. M. Girvan, C. W. Levy, P. Williams, K. Fisher, M. R. Cheesman, S. E. Rigby, D. Leys, A. W. Munro
Glutamate-Haem Ester Bond Formation Is Disfavoured In Flavocytochrome P450 Bm3: Characterization Of Glutamate Substitution Mutants At The Haem Site Of P450 Bm3.
Biochem. J. V. 427 455 2010
PubMed-ID: 20180779 | Reference-DOI: 10.1042/BJ20091603

Molecule 1 - BIFUNCTIONAL P-450/NADPH-P450 REDUCTASE
	Chains	:	A, B
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	TG1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HEME DOMAIN (UNP RESIDUES 2-471)
	Gene	:	CYP102A1, CYP102
	Mutation	:	YES
	Organism Scientific	:	BACILLUS MEGATERIUM
	Organism Taxid	:	1404
	Synonym	:	FLAVOCYTOCHROME P450 BM3, CYTOCHROME P450(BM-3), P450BM-3, CYTOCHROME P450 102, NADPH--CYTOCHROME P450 REDUCTASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	140	2	Ligand/Ion	N-PALMITOYLGLYCINE
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	140	1	Ligand/Ion	N-PALMITOYLGLYCINE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	140	1	Ligand/Ion	N-PALMITOYLGLYCINE
2	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:69 , LEU A:75 , GLU A:86 , PHE A:87 , TRP A:96 , HIS A:100 , PHE A:107 , PHE A:261 , ALA A:264 , GLY A:265 , THR A:268 , THR A:269 , PHE A:331 , PRO A:392 , PHE A:393 , GLY A:394 , ARG A:398 , ALA A:399 , CYS A:400 , ILE A:401 , ALA A:406 , HOH A:477 , HOH A:478 , HOH A:480 , HOH A:481 , HOH A:510 , HOH A:569 , HOH A:1255	BINDING SITE FOR RESIDUE HEM A 471
2	AC2	SOFTWARE	LEU A:29 , TYR A:51 , SER A:72 , GLN A:73 , ALA A:74 , VAL A:78 , ALA A:82 , LEU A:188 , HOH A:660 , HOH A:832	BINDING SITE FOR RESIDUE 140 A 1470
3	AC3	SOFTWARE	LYS B:69 , GLU B:86 , PHE B:87 , TRP B:96 , HIS B:100 , PHE B:261 , ALA B:264 , GLY B:265 , THR B:268 , THR B:269 , THR B:327 , PHE B:331 , PRO B:392 , PHE B:393 , GLY B:394 , ARG B:398 , ALA B:399 , CYS B:400 , ILE B:401 , GLY B:402 , PHE B:405 , ALA B:406 , HOH B:472 , HOH B:483 , HOH B:491 , HOH B:494 , HOH B:548 , HOH B:618 , HOH B:1254	BINDING SITE FOR RESIDUE HEM B 471
4	AC4	SOFTWARE	LEU B:29 , ARG B:47 , TYR B:51 , SER B:72 , GLN B:73 , ALA B:74 , LEU B:188 , LEU B:437 , HOH B:566	BINDING SITE FOR RESIDUE 140 B 1470

(no "SS Bond" information available for 3KX3)

(no "Cis Peptide Bond" information available for 3KX3)

(no "SAP(SNP)/Variant" information available for 3KX3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CPXB_BACMB	394-403	2	A:393-402 B:393-402

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CPXB_BACMB	394-403	1	A:393-402 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CPXB_BACMB	394-403	1	- B:393-402

(no "Exon" information available for 3KX3)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:454
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:456
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
           CPXB_BACMB     4 KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 459
               SCOP domains d3kx3a_ A: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3kx3A00 A:3-458 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--...hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eeehhheee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kx3 A   3 KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGEFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKAS--QSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 458
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   |  |232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      
                                                                                                                                                                                                                                                         226  |                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                            229

Chain B from PDB  Type:PROTEIN  Length:456
 aligned with CPXB_BACMB | P14779 from UniProtKB/Swiss-Prot  Length:1049

    Alignment length:456
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
           CPXB_BACMB     4 KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGLFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 459
               SCOP domains d3kx3b_ B: Cytochrome P450 bm-3                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3kx3B00 B:3-458 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhh....eeee.hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeee...eee...eee....eeeeehhhhh.hhhhhh......hhhhhhhhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhheeee........eee...eee...eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kx3 B   3 KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYLSSQRLIKEACDESRFDKNLSQALKFVRDFAGDGEFTSWTHEKNWKKAHNILLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDTIGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENKRQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDENIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPVPSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDELMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIGQQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKKIPLGGI 458
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: Cytochrome P450 (323)

Protein domain: Cytochrome P450 bm-3 (60)

Bacillus megaterium [TaxId: 1404] (60)

1a	d3kx3a_	A:
1b	d3kx3b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Bacillus megaterium. Organism_taxid: 1404. (20)

1a	3kx3A00	A:3-458
1b	3kx3B00	B:3-458

(no "Pfam Domain" information available for 3KX3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CPXB_BACMB | P14779)

molecular function
	GO:0010181	FMN binding	Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0003958	NADPH-hemoprotein reductase activity	Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
	GO:0070330	aromatase activity	Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0016712	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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